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Barbier J, Vaillant C, Volff JN, Brunet FG, Audit B. Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution. Genes (Basel) 2021; 12:genes12060851. [PMID: 34205881 PMCID: PMC8228248 DOI: 10.3390/genes12060851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequence has an influence on the position of nucleosomes on genomes, although other factors are also implicated, such as ATP-dependent remodelers or competition of the nucleosome with DNA binding proteins. Different sequence motifs can promote or inhibit the nucleosome formation, thus influencing the accessibility to the DNA. Sequence-encoded nucleosome positioning having functional consequences on cell processes can then be selected or counter-selected during evolution. We review the interplay between sequence evolution and nucleosome positioning evolution. We first focus on the different ways to encode nucleosome positions in the DNA sequence, and to which extent these mechanisms are responsible of genome-wide nucleosome positioning in vivo. Then, we discuss the findings about selection of sequences for their nucleosomal properties. Finally, we illustrate how the nucleosome can directly influence sequence evolution through its interactions with DNA damage and repair mechanisms. This review aims to provide an overview of the mutual influence of sequence evolution and nucleosome positioning evolution, possibly leading to complex evolutionary dynamics.
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Affiliation(s)
- Jérémy Barbier
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
| | - Cédric Vaillant
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
- Correspondence: (J.-N.V.); (B.A.)
| | - Frédéric G. Brunet
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
| | - Benjamin Audit
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
- Correspondence: (J.-N.V.); (B.A.)
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Duan B, Ding P, Navarre WW, Liu J, Xia B. Xenogeneic Silencing and Bacterial Genome Evolution: Mechanisms for DNA Recognition Imply Multifaceted Roles of Xenogeneic Silencers. Mol Biol Evol 2021; 38:4135-4148. [PMID: 34003286 PMCID: PMC8476142 DOI: 10.1093/molbev/msab136] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/08/2021] [Indexed: 12/14/2022] Open
Abstract
Horizontal gene transfer (HGT) is a major driving force for bacterial evolution. To avoid the deleterious effects due to the unregulated expression of newly acquired foreign genes, bacteria have evolved specific proteins named xenogeneic silencers to recognize foreign DNA sequences and suppress their transcription. As there is considerable diversity in genomic base compositions among bacteria, how xenogeneic silencers distinguish self- from nonself DNA in different bacteria remains poorly understood. This review summarizes the progress in studying the DNA binding preferences and the underlying molecular mechanisms of known xenogeneic silencer families, represented by H-NS of Escherichia coli, Lsr2 of Mycobacterium, MvaT of Pseudomonas, and Rok of Bacillus. Comparative analyses of the published data indicate that the differences in DNA recognition mechanisms enable these xenogeneic silencers to have clear characteristics in DNA sequence preferences, which are further correlated with different host genomic features. These correlations provide insights into the mechanisms of how these xenogeneic silencers selectively target foreign DNA in different genomic backgrounds. Furthermore, it is revealed that the genomic AT contents of bacterial species with the same xenogeneic silencer family proteins are distributed in a limited range and are generally lower than those species without any known xenogeneic silencers in the same phylum/class/genus, indicating that xenogeneic silencers have multifaceted roles on bacterial genome evolution. In addition to regulating horizontal gene transfer, xenogeneic silencers also act as a selective force against the GC to AT mutational bias found in bacterial genomes and help the host genomic AT contents maintained at relatively low levels.
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Affiliation(s)
- Bo Duan
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
| | - William Wiley Navarre
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
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Jia Y, Li H, Wang J, Meng H, Yang Z. Spectrum structures and biological functions of 8-mers in the human genome. Genomics 2018. [PMID: 29522801 DOI: 10.1016/j.ygeno.2018.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The spectra of k-mer frequencies can reveal the structures and evolution of genome sequences. We confirmed that the trimodal spectrum of 8-mers in human genome sequences is distinguished only by CG2, CG1 and CG0 8-mer sets, containing 2,1 or 0 CpG, respectively. This phenomenon is called independent selection law. The three types of CG 8-mers were considered as different functional elements. We conjectured that (1) nucleosome binding motifs are mainly characterized by CG1 8-mers and (2) the core structural units of CpG island sequences are predominantly characterized by CG2 8-mers. To validate our conjectures, nucleosome occupied sequences and CGI sequences were extracted, then the sequence parameters were constructed through the information of the three CG 8-mer sets respectively. ROC analysis showed that CG1 8-mers are more preference in nucleosome occupied segments (AUC > 0.7) and CG2 8-mers are more preference in CGI sequences (AUC > 0.99). This validates our conjecture in principle.
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Affiliation(s)
- Yun Jia
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China; College of Science, Inner Mongolia University of Technology, Hohhot 010051, China
| | - Hong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
| | - Jingfeng Wang
- College of Science, Inner Mongolia University of Technology, Hohhot 010051, China
| | - Hu Meng
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Zhenhua Yang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
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Balakrishnan L, Milavetz B. Epigenetic Regulation of Viral Biological Processes. Viruses 2017; 9:v9110346. [PMID: 29149060 PMCID: PMC5707553 DOI: 10.3390/v9110346] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/13/2017] [Accepted: 11/15/2017] [Indexed: 12/21/2022] Open
Abstract
It is increasingly clear that DNA viruses exploit cellular epigenetic processes to control their life cycles during infection. This review will address epigenetic regulation in members of the polyomaviruses, adenoviruses, human papillomaviruses, hepatitis B, and herpes viruses. For each type of virus, what is known about the roles of DNA methylation, histone modifications, nucleosome positioning, and regulatory RNA in epigenetic regulation of the virus infection will be discussed. The mechanisms used by certain viruses to dysregulate the host cell through manipulation of epigenetic processes and the role of cellular cofactors such as BRD4 that are known to be involved in epigenetic regulation of host cell pathways will also be covered. Specifically, this review will focus on the role of epigenetic regulation in maintaining viral episomes through the generation of chromatin, temporally controlling transcription from viral genes during the course of an infection, regulating latency and the switch to a lytic infection, and global dysregulation of cellular function.
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Affiliation(s)
- Lata Balakrishnan
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA.
| | - Barry Milavetz
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA.
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Nishida H, Oshima T. Archaeal histone distribution is associated with archaeal genome base composition. J GEN APPL MICROBIOL 2016; 63:28-35. [PMID: 27990001 DOI: 10.2323/jgam.2016.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A subpopulation of Archaea possesses histones, which are similar to eukaryotic histones H3 and H4. However, archaeal histones are smaller than H3 and H4, and are not post-translationally modified. In addition, the fundamental unit of archaeal histones might be a dimer. The organization of archaeal nucleosomes, therefore, differs from that of eukaryotic nucleosomes. The base compositions of archaeal genome are much more diversified than those of eukaryote and the archaeal histones have more diversified amino acid sequences, which are reflected by their varied isoelectric points. We hypothesized that the highly diversified archaeal genomic DNA base composition may cause the archaeal histone variation. Phylogenetic analysis revealed that the distribution of archaeal histones is associated with their genomic DNA base composition. This result strongly suggests that archaeal histones have evolved concomitantly with their genomic DNA base composition. Eukaryotic histones are one of the most evolutionarily conserved proteins and would limit the diversification of genomic DNA base composition. In contrast, archaeal histones have diversified and would permit the great diversification of genomic DNA base composition.
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Affiliation(s)
- Hiromi Nishida
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University
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Nishida H. Relationship between chromosomal GC content and isoelectric points of histones in fungi. J GEN APPL MICROBIOL 2015; 61:24-6. [PMID: 25833677 DOI: 10.2323/jgam.61.24] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Hiromi Nishida
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University
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Hettiarachchi N, Kryukov K, Sumiyama K, Saitou N. Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning. Genome Biol Evol 2014; 6:2527-42. [PMID: 25364802 PMCID: PMC4202324 DOI: 10.1093/gbe/evu188] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2014] [Indexed: 01/01/2023] Open
Abstract
Many studies on conserved noncoding sequences (CNSs) have found that CNSs are enriched significantly in regulatory sequence elements. We conducted whole-genome analysis on plant CNSs to identify lineage-specific CNSs in eudicots, monocots, angiosperms,and vascular plants based on the premise that lineage-specific CNSs define lineage-specific characters and functions in groups of organisms. We identified 27 eudicot, 204 monocot, 6,536 grass, 19 angiosperm, and 2 vascular plant lineage-specific CNSs(lengths range from 16 to 1,517 bp) that presumably originated in their respective common ancestors. A stronger constraint on the CNSs located in the untranslated regions was observed. The CNSs were often flanked by genes involved in transcription regulation. A drop of A+T content near the border of CNSs was observed and CNS regions showed a higher nucleosome occupancy probability. These CNSs are candidate regulatory elements, which are expected to define lineage-specific features of various plant groups.
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Affiliation(s)
- Nilmini Hettiarachchi
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Kirill Kryukov
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Kenta Sumiyama
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Naruya Saitou
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
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Nishida H. Evolution of genome base composition and genome size in bacteria. Front Microbiol 2012; 3:420. [PMID: 23230432 PMCID: PMC3515811 DOI: 10.3389/fmicb.2012.00420] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 11/21/2012] [Indexed: 11/13/2022] Open
Affiliation(s)
- Hiromi Nishida
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo Tokyo, Japan
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